I've had my frustrations with both, but I haven't found an alternative that does everything we need and isn't way more expensive. Things I need to do, outside of the usual:

   - time tracking
   - detailed planning/reporting (we use Greenhopper)
   - customer service (hiding projects and fields for internal use)
   - integration with version control

We use a few plugins, but not many, and the whole 10 users for $10 is pretty amazing. By the time you need more, you can afford it. I also like FogBugz/Kiln, but the price is much higher for 3-10 users (OnDemand gives 2 free to startups and students).

By far, my biggest complaint to Atlassian is upgrades, which are a huge PITA. There has to be an amazing new feature for me to go through that.